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Information on EC 2.1.1.228 - tRNA (guanine37-N1)-methyltransferase and Organism(s) Methanocaldococcus jannaschii and UniProt Accession Q58293
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2.1.1.228 tRNA (guanine37-N1)-methyltransferaseIUBMB Comments
This enzyme is important for the maintenance of the correct reading frame during translation. Unlike TrmD from Escherichia coli, which recognizes the G36pG37 motif preferentially, the human enzyme (encoded by TRMT5) also methylates inosine at position 37 .
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Word Map
- 2.1.1.228
- methyltransferases
-
anticodon
- adomet
- 1-methylguanosine
- drug development
-
n2-guanine
- trmt10a
- 1-methyladenine
-
adomet-dependent
- 5-methyluridine
- trmfo
-
n1-methylation
-
methyl-deficient
- 7-methylguanine
-
spout
-
epitranscriptome
-
nsun2-mediated
- medicine
The taxonomic range for the selected organisms is: Methanocaldococcus jannaschii
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
+
guanine37 in tRNA
=
+
N1-methylguanine37 in tRNA
Synonyms
trna methyltransferase, trna(m1g37)methyltransferase, patrmd, trna(m(1)g37)methyltransferase, trm5p, patrm5a, trna (m1g37) methyltransferase, trmt5, attrm5a, patrm5b, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + guanine37 in tRNA = S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5 involving proton abstraction during docking of G37 in the active site by a general base , E185
S-adenosyl-L-methionine + guanine37 in tRNA = S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
substrate recognition and reaction mechanisms, overview
-
PATHWAY SOURCE
PATHWAYS
-
-, -, -
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:tRNA (guanine37-N1)-methyltransferase
This enzyme is important for the maintenance of the correct reading frame during translation. Unlike TrmD from Escherichia coli, which recognizes the G36pG37 motif preferentially, the human enzyme (encoded by TRMT5) also methylates inosine at position 37 [4].
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + guanine37 in Methanocaldococcus jannaschii tRNA(Cys)
S-adenosyl-L-homocysteine + N1-methylguanine37 in Methanocaldococcus jannaschii tRNA(Cys)
-
-
-
?
S-adenosyl-L-methionine + guanine37 in Methanocaldococcus jannaschii tRNAArg(UCG)
S-adenosyl-L-homocysteine + N1-methylguanine37 in Methanocaldococcus jannaschii tRNAArg(UCG)
possessing the sequence G36G37
-
-
?
S-adenosyl-L-methionine + guanine37 in Methanocaldococcus jannaschii tRNACys
S-adenosyl-L-homocysteine + N1-methylguanine37 in Methanocaldococcus jannaschii tRNACys
-
-
-
?
S-adenosyl-L-methionine + guanine37 in Methanocaldococcus jannaschii tRNACys(GCA)
S-adenosyl-L-homocysteine + N1-methylguanine37 in Methanocaldococcus jannaschii tRNACys(GCA)
possessing the sequence A36G37. The enzyme is inactive with mutant forms of Methanocaldococcus jannaschii tRNACys(GCA) containing A37, C37, or U37
-
-
?
S-adenosyl-L-methionine + guanine37 in Methanocaldococcus jannaschii tRNAGlu(UUC)
S-adenosyl-L-homocysteine + N1-methylguanine37 in Methanocaldococcus jannaschii tRNAGlu(UUC)
possessing the sequence C36G37
-
-
?
S-adenosyl-L-methionine + guanine37 in Methanocaldococcus jannaschii tRNALeu(UCG)
S-adenosyl-L-homocysteine + N1-methylguanine37 in Methanocaldococcus jannaschii tRNALeu(UCG)
possessing the sequence G36G37
-
-
?
S-adenosyl-L-methionine + guanine37 in Methanocaldococcus jannaschii tRNAPro
S-adenosyl-L-homocysteine + N1-methylguanine37 in Methanocaldococcus jannaschii tRNAPro
-
-
-
?
S-adenosyl-L-methionine + guanine37 in Methanocaldococcus jannaschii tRNAPro(GGG)
S-adenosyl-L-homocysteine + N1-methylguanine37 in Methanocaldococcus jannaschii tRNAPro(GGG)
possessing the sequence G36G37
-
-
?
S-adenosyl-L-methionine + guanine37 in Methanocaldococcus jannaschii tRNAPro(UGG)
S-adenosyl-L-homocysteine + N1-methylguanine37 in Methanocaldococcus jannaschii tRNAPro(UGG)
possessing the sequence G36G37
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNACys
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNACys
Methanococcus jannaschii tRNACys
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAPhe
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPhe
-
-
-
?
S-adenosyl-L-methionine + guanine36 in tRNALeu
S-adenosyl-L-homocysteine + N1-methylguanine36 in tRNALeu
-
G36-substituted tRNA substrate Escherichia coli tRNALeu, Trm5 shows a lack of discrimination between the two sequences of G36 and G37
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
S-adenosyl-L-methionine + guanine37 in tRNACys
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNACys
-
Methanococcus jannaschii tRNACys
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
tight binding of Trm5 to products
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
Trm5 recognizes N1 and O6 of G37, but the exocyclic 2-amino group of G37 is dispensable for Trm5. Trm5 does not require G36
-
-
?
additional information
?
-
the enzyme is specific for methylation of guanine37 in tRNA. No methylation of tRNAArg(UCU) possessing the sequence U36G37
-
-
?
additional information
?
-
-
the enzyme is specific for methylation of guanine37 in tRNA. No methylation of tRNAArg(UCU) possessing the sequence U36G37
-
-
?
additional information
?
-
structure of Trm5 active site bound to tRNA and S-adenosyl-L-methionine, induced fit for active-site assembly, detailed overview. E185 is crucial both for general base catalysis and for the conformational change that precedes catalysis
-
-
?
additional information
?
-
radioactive assay method development and evaluation using labeled S-adenosyl-L-methionine and unlabeled tRNA, detailed overview. The slow step of the Trm5 reaction is after methyl transfer and is associated with release of the m1G37-tRNA product
-
-
-
additional information
?
-
structural basis for substrate recognition, the D1 domain of the enzyme undergoes large conformational changes upon the binding of tRNA, the enzyme recognizes the overall shape of tRNA, overview. Enzyme-substrate interactions in the catalytic domain, D1 domain ofMjTrm5b transitions, overview
-
-
-
additional information
?
-
the mutant tRNAMet transcripts (G37) are modified with m1G37 modification by the Mj-Trm5 but as less efficiently as cytoplasmic tRNALeu(CAG) transcripts. In contrast, the modification is not detected in the human wild-type tRNAMet transcripts (A37) in the presence of Mj-Trm5. The human cytoplasmic tRNALeu(CAG) transcripts (G37) are modified by the Mj-Trm5, whereas human cytoplasmic tRNAThr transcripts (A37) are not modified in the presence of Mj-Trm5. Marked decrease in the steady-state levels of mutated tRNAMet
-
-
-
additional information
?
-
tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA
-
-
-
additional information
?
-
-
Trm5 catalyzes methyl transfer to synthesize the m1G37 base at the 3' position adjacent to the tRNA anticodon
-
-
?
additional information
?
-
-
recognition of N1 of G37 in tRNA is essential for translational fidelity in all biological domains, Trm5 shows a less rigid requirement of guanosine functional groups. Replacment of functional groups of G37 by guanosine analogues, i.e. deoxyG, 6-thioG, inosine, and 2-aminopurine, in MjtRNACys, to design the optimal substrate for Trm5
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAPhe
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPhe
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
-
?
additional information
?
-
-
Trm5 catalyzes methyl transfer to synthesize the m1G37 base at the 3' position adjacent to the tRNA anticodon
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
S-adenosyl-L-methionine
-
S-adenosyl-L-methionine
-
Trm5 binding structure, detailed overview
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
S-adenosyl-L-homocysteine
-
an S-adenosyl-L-methionine analogue
additional information
-
fragments of S-adenosyl-L-methionine, adenosine and methionine, are poor inhibitors of Trm5, while they are selectve inhibitors for TrmD from Escherichia coli
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00028
guanine37 in Methanocaldococcus jannaschii tRNA(Cys)
pH 8.0, 50°C
-
0.0012
guanine37 in Methanocaldococcus jannaschii tRNAPro
pH 8.0, 52°C
-
0.0007
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, wild-type enzyme
-
0.0025
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme Y176A
-
0.003
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme D223A
-
0.003
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme P226A
-
0.0043
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme R144A
-
0.0046
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme G205A/G207A
-
0.006
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme P267A
-
0.0072
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme N225A
-
0.0083
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme N265A
-
0.0005
S-adenosyl-L-methionine
pH 8.0, 50°C, mutant enzyme P267A
0.001
S-adenosyl-L-methionine
pH 8.0, 50°C, wild-type enzyme
additional information
additional information
kinetic analysis of tRNA truncation mutants and tRNA mutant with alterations in the anticodon loop reveals that TrmD and Trm5 exhibit separate and distinct mode of tRNA recognition, suggesting that they evolved by independent and nonoverlapping pathways from their unrelated AdoMet families
-
additional information
additional information
Michaelis-Menten kinetic analysis
-
additional information
additional information
wild-type and mutant enzymes pH-dependence of the single-turnover rate constant: the pH dependence of kobs in single-turnover analysis corresponds to proton ransfer during a slower process of induced fit, rather than the bond-breaking and bond-forming steps of methyl transfer, detailed analysis and overview
-
additional information
additional information
pre-steady-state and steady-state Michaelis-Menten kinetics, single turnover assays
-
additional information
additional information
-
pre-steady-state and steady-state kinetics, rapid burst phase followed by a slower and linear phase in reaction, single-turnover and from steady-state analysis, overview
-
additional information
additional information
-
S-adenosyl-L-methionine and adenosine binding kinetics and kinetic analysis of enzyme reaction, overview
-
additional information
additional information
-
single turnover kinetics and thermodynamic analysis of effect of different guanosine analogues on m1G37-tRNA synthesis, kinetic analysis, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.01
guanine37 in Methanocaldococcus jannaschii tRNA(Cys)
pH 8.0, 50°C
-
0.0086
guanine37 in Methanocaldococcus jannaschii tRNAPro
pH 8.0, 52°C
-
0.02
S-adenosyl-L-methionine
-
kcat in steady-state phase turnover, pH and temperature not specified in the publication
0.0001
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme P267A
-
0.0003
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme D223A
-
0.0013
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme N265A
-
0.0013
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme Y176A
-
0.0015
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme G205A/G207A
-
0.0018
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme P226A
-
0.003
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme R144A
-
0.0037
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme N225A
-
0.0083
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, wild-type enzyme
-
0.0001
S-adenosyl-L-methionine
pH 8.0, 50°C, mutant enzyme P267A
0.012
S-adenosyl-L-methionine
pH 8.0, 50°C, wild-type enzyme
additional information
additional information
kinetic analysis of tRNA truncation mutants and tRNA mutant with alterations in the anticodon loop reveals that TrmD and Trm5 exhibit separate and distinct mode of tRNA recognition, suggesting that they evolved by independent and nonoverlapping pathways from their unrelated AdoMet families
-
additional information
additional information
-
0.12 is kchem in the first rapid burst turnover
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
36.9
guanine37 in Methanocaldococcus jannaschii tRNA(Cys)
pH 8.0, 50°C
-
7.22
guanine37 in Methanocaldococcus jannaschii tRNAPro
pH 8.0, 52°C
-
additional information
additional information
kinetic analysis of tRNA truncation mutants and tRNA mutant with alterations in the anticodon loop reveals that TrmD and Trm5 exhibit separate and distinct mode of tRNA recognition, suggesting that they evolved by independent and nonoverlapping pathways from their unrelated AdoMet families
-
0.017
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme P267A
-
0.11
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme D223A
-
0.16
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme N265A
-
0.32
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme G205A/G207A
-
0.51
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme N225A
-
0.53
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme Y176A
-
0.61
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme P226A
-
0.775
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, mutant enzyme R144A
-
11.9
guanine37 in Methanocaldococcus jannaschii tRNACys
pH 8.0, 50°C, wild-type enzyme
-
0.2
S-adenosyl-L-methionine
pH 8.0, 50°C, mutant enzyme P267A
12.2
S-adenosyl-L-methionine
pH 8.0, 50°C, wild-type enzyme
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.014
5'-[(2-aminoethyl)thio]-5'-deoxy-adenosine
-
pH not specified in the publication, 55°C
0.461
6-Chloropurine
-
pH not specified in the publication, 55°C
0.0012
methylthioadenosine
-
pH not specified in the publication, 55°C
0.00049
S-adenosyl-L-homocysteine
-
pH not specified in the publication, 55°C
44
S-methyl-L-cysteine
-
pH not specified in the publication, 55°C
additional information
additional information
-
inhibition kinetics of S-adenosyl-L-methionine analogues, overview
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 9.8
preincubation of Trm5 at pH 6.0, followed by adjustment of the solution to pH 8.0, does not cause irreversible inactivation of the enzyme. Enzyme treated in this manner retained equivalent activity in single-turnover assay
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
85°C is the optimal growth temperature
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
the tRNA mutations, that disrupt the G19:C56 base pair, reduce the activity of full-length Trm5 at 70°C by enhancing the KM values but maintaining the kcat values. The Trm5 mutant with alanine substitutions of the D1 residues, that interact with the tRNA outer corner, has a higher KM value than the wild-type Trm5
metabolism
a hypertension-associated mitochondrial DNA mutation introduces an m1G37 mutation 4435A->G into human mitochondrial tRNAMet, altering its structure and function, phenotype and pathogenic molecular mechanism, overview. The mutation affects a highly conserved adenosine at position 37, 3' adjacent to the tRNA's anticodon, which is important for the fidelity of codon recognition and stabilization. Defective nucleotide modifications of mitochondrial tRNAs are associated with several human diseases. Trm5 is one of the tRNA (m1G37)-methyltransferases that catalyzes the identical tRNA modification, m1G37
physiological function
additional information
evolution
at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. Trm5 belongs to the class I tRNA methyl transferases. Trm5 is an active monomer that uses the class I-fold. MjTrm5 is homologous to human Trm5
evolution
the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Phylogenetic analyses reveals that the archaeal Trm5s can be classified into three categories: Trm5a, Trm5b, and Trm5c. Trm5a, Trm5b, and Trm5c all perform the N1-methylation of tRNA G37. Enzyme Trm5 belongs to the class I methyltransferases. The Methanocaldococcus jannaschii Trm5b residues involved in the G19:C56 recognition are not conserved in Pyroccocus abyssi Trm5a
physiological function
modification at guanine37 is important for maintaining the reading frame fidelity
physiological function
the m1G37 modification prevents tRNA frameshifts on the ribosome by assuring correct codon-anticodon pairings, and thus is essential for the fidelity of protein synthesis
physiological function
he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
physiological function
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
additional information
evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
additional information
structure comparison of the Pyrococcus abyssii Trm5a enzyme structure (PDB IDs 5HJJ and 5WT1) with the structure of its orthologue Trm5b (MjTrm5b, PDB IDs 2YX1 and 3AY0) from Methanococcus jannaschii, overview
additional information
Trm5 consists of three structural domains: domain 1 (D1), domain 2 (D2), and domain 3 (D3). D1 corresponds to the less-conserved region among Trm5 enzymes from all species, while D2 corresponds to the conserved region. The structure of D2 shares homology with that of TYW2, the tRNA-wybutosine (yW) synthesizing enzyme-2. D3 corresponds to the Rossmann-fold domain containing the AdoMet binding site, and is conserved among the class-I MTases. The D2-D3 fragment alone possesses methyl-transfer activity comparable to that of the full-length enzyme, although the presence of D1 lowers and enhances the KM and kcat values (the Michaelis and catalytic rate constants, respectively, in the Michaelis-Menten equation) for tRNA, respectively, as compared to the D2-D3 fragment. Function of D1, overview. The interaction between the outer-corner of the tRNA and Trm5 D1 is essential to confer sufficiently robust affinity for the tRNA at physiological temperatures
additional information
-
S-adenosyl-methionine-dependent m1G37-tRNA methyltransferases rapidly screen tRNA by direct recognition of G37 in order to monitor the global state of m1G37-tRNA
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
analysis of enzyme complex structures of Trm5b (MjTrm5b, PDB IDs 2YX1 and 3AY0) from Methanococcus jannaschii
analysis of the crystal structure of the Trm5-tRNA-AdoMet ternary complex
crystal structure of Trm5 in complex with the methyl donor analogue sinefungin at 2.2 A resolution, vapor diffusion method at 20°C
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D223A
D223E
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
D223L
site-directed mutagenesis, the mutant shows complete loss of activity
D223N
site-directed mutagenesis, the mutant shows complete loss of activity
E185A
site-directed mutagenesis, the mutant shows complete loss of activity
E185D
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
E185Q
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
G205A/G207A
K137A
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
K318A
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
N225A
kcat/Km for guanine37 in Methanocaldococcus jannaschii tRNACys is 5% of the wild-type value
N265A
N265H
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
N265Q
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
P226A
kcat/Km for guanine37 in Methanocaldococcus jannaschii tRNACys is 6% of the wild-type value
P267A
R144A
kcat/Km for guanine37 in Methanocaldococcus jannaschii tRNACys is 6% of the wild-type value
R145A
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
R181A
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
R186A
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
Y176A
kcat/Km for guanine37 in Methanocaldococcus jannaschii tRNACys is 5% of the wild-type value
Y177A
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
Y177F
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
additional information
D223A
kcat/Km for guanine37 in Methanocaldococcus jannaschii tRNACys is 1% of the wild-type value
D223A
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
G205A/G207A
kcat/Km for guanine37 in Methanocaldococcus jannaschii tRNACys is 3% of the wild-type value
N265A
kcat/Km for guanine37 in Methanocaldococcus jannaschii tRNACys is 1% of the wild-type value
N265A
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
P267A
kcat/Km for guanine37 in Methanocaldococcus jannaschii tRNACys is 0.1% of the wild-type value
P267A
site-directed mutagenesis, the mutant shows altered single turnover kinetics compared to the wild-type enzyme
additional information
proline at position 267 is a critical residue for catalysis, because substitution of this residue severely decreases kcat of the methylation reaction in steady-state kinetic analysis. However, substitution of P267 has milder effect on Km and little effect on Kd of either substrate. Because P267 has no functional side chain that can directly participate in the chemistry of methyl transfer, we suggest that its role in catalysis is to stabilize conformations of enzyme and substrates for proper alignment of reactive groups at the enzyme active site. Sequence analysis shows that P267 is embedded in a peptide motif that is conserved among the Trm5 family, but absent from the TrmD family, supporting the notion that the two families are descendants of unrelated protein structures
additional information
the m.4435A->G mutation introduces an m1G37 modification of tRNAMet, altering its structure and function. Primer extension and methylation activity assays indeed confirm that the m.4435A3G mutation creates a tRNA methyltransferase 5 (TRMT5)-catalyzed m1G37 modification of tRNAMet
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
the sequence and structural distinction of bacterial TrmD from the eukaryotic Trm5 suggests that strategies can be developed to specifically inhibit TrmD without a deleterious effect on humans
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Christian, T.; Evilia, C.; Williams, S.; Hou, Y.M.
Distinct origins of tRNA(m1G37) methyltransferase
J. Mol. Biol.
339
707-719
2004
Methanocaldococcus jannaschii (Q58293), Methanocaldococcus jannaschii
Goto-Ito, S.; Ito, T.; Ishii, R.; Muto, Y.; Bessho, Y.; Yokoyama, S.
Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5
Proteins
72
1274-1289
2008
Methanocaldococcus jannaschii (Q58293), Methanocaldococcus jannaschii
Christian, T.; Evilia, C.; Hou, Y.M.
Catalysis by the second class of tRNA(m1G37) methyl transferase requires a conserved proline
Biochemistry
45
7463-7473
2006
Methanocaldococcus jannaschii (Q58293)
Christian, T.; Hou, Y.M.
Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases
J. Mol. Biol.
373
623-632
2007
Escherichia coli, Methanocaldococcus jannaschii (Q58293)
Christian, T.; Lahoud, G.; Liu, C.; Hou, Y.M.
Control of catalytic cycle by a pair of analogous tRNA modification enzymes
J. Mol. Biol.
400
204-217
2010
Escherichia coli, Methanocaldococcus jannaschii
Christian, T.; Lahoud, G.; Liu, C.; Hoffmann, K.; Perona, J.J.; Hou, Y.M.
Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5
RNA
16
2484-2492
2010
Methanocaldococcus jannaschii (Q58293)
Lahoud, G.; Goto-Ito, S.; Yoshida, K.; Ito, T.; Yokoyama, S.; Hou, Y.M.
Differentiating analogous tRNA methyltransferases by fragments of the methyl donor
RNA
17
1236-1246
2011
Escherichia coli, Methanocaldococcus jannaschii
Sakaguchi, R.; Giessing, A.; Dai, Q.; Lahoud, G.; Liutkeviciute, Z.; Klimasauskas, S.; Piccirilli, J.; Kirpekar, F.; Hou, Y.M.
Recognition of guanosine by dissimilar tRNA methyltransferases
RNA
18
1687-1701
2012
Escherichia coli, Methanocaldococcus jannaschii
Goto-Ito, S.; Ito, T.; Yokoyama, S.
Trm5 and TrmD two enzymes from distinct origins catalyze the identical tRNA modification, m1G37
Biomolecules
7
32
2017
Escherichia coli (P0A873), Haemophilus influenzae (P43912), Haemophilus influenzae ATCC 51907 (P43912), Haemophilus influenzae DSM 11121 (P43912), Haemophilus influenzae KW20 (P43912), Haemophilus influenzae RD (P43912), Methanocaldococcus jannaschii (Q58293), Methanocaldococcus jannaschii ATCC 43067 (Q58293), Methanocaldococcus jannaschii DSM 2661 (Q58293), Methanocaldococcus jannaschii JAL-1 (Q58293), Methanocaldococcus jannaschii JCM 10045 (Q58293), Methanocaldococcus jannaschii NBRC 100440 (Q58293), Pyrococcus abyssi (Q9V2G1), Pyrococcus abyssi Orsay (Q9V2G1)
Zhou, M.; Xue, L.; Chen, Y.; Li, H.; He, Q.; Wang, B.; Meng, F.; Wang, M.; Guan, M.X.
A hypertension-associated mitochondrial DNA mutation introduces an m1G37 modification into tRNAMet, altering its structure and function
J. Biol. Chem.
293
1425-1438
2018
Methanocaldococcus jannaschii (Q58293), Methanocaldococcus jannaschii ATCC 43067 (Q58293), Methanocaldococcus jannaschii DSM 2661 (Q58293), Methanocaldococcus jannaschii JAL-1 (Q58293), Methanocaldococcus jannaschii JCM 10045 (Q58293), Methanocaldococcus jannaschii NBRC 100440 (Q58293)
Hou, Y.M.; Masuda, I.
Kinetic analysis of tRNA methyltransferases
Methods Enzymol.
560
91-116
2015
Escherichia coli (P0A873), Haemophilus influenzae (P43912), Haemophilus influenzae ATCC 51907 (P43912), Haemophilus influenzae DSM 11121 (P43912), Haemophilus influenzae KW20 (P43912), Haemophilus influenzae RD (P43912), Homo sapiens (Q32P41), Methanocaldococcus jannaschii (Q58293), Methanocaldococcus jannaschii ATCC 43067 (Q58293), Methanocaldococcus jannaschii DSM 2661 (Q58293), Methanocaldococcus jannaschii JAL-1 (Q58293), Methanocaldococcus jannaschii JCM 10045 (Q58293), Methanocaldococcus jannaschii NBRC 100440 (Q58293)
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